Thank you David and Arneh for the comments. I just have a couple of things i want to clarify about the constrain distances i used. The distance I used to pull the ligand and receptor apart was a non-bonded distance between the amide nitrogen of the ligand and the oxygen carbonyl of the receptor (on both ends). looking at the slowgrowth results of my 5 ns, the distances i specifed increased from lambda 0 to 1, however, I didnt get separation as I wanted it since the ends just separated and the middle interaction of the ligand-receptor stayed intact. nothing unusal happened to the ligand or receptor. I dont think my method altered the internal degrees of freedom of the ligand. Can you please clarify this issue for me.
I used constraint=all-bonds in my mdp file. Again, thanks you both for the comments. Belquis > >> >> Maybe it should be obvious, but (a) why are you constraining two >> distances, and (b) are you sure your constraints aren't going to muck >> with the internal degrees of freedom for the ligand? I would think one >> would like to pull the ligand out of the receptor along some >> particular direction, but without doing anything to alter its internal >> degrees of freedom, or there would be a free energy associated with >> changing its internal degrees of freedom that you wouldn't capture in >> the PMF calculation. >> > > I agree with David's comments here. Check out the 'Special Topic' > section > of the GMX manual. you can either do a pulling simulation or umbrella > sampling (where the position and constrain the ligand on some rxn > coordinate, in several simulation). The output of such simulatsions is a > *.pdo file, which you can then run g_wham on to obtain a PMF. > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
